Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change
Open accessAbstract
Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.
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Models that do not account for past population size changes have the potential to overestimate divergence times.
“suggesting that models that do not account for past population size changes have the potential to overestimate divergence times (e.g. Hailer et al., 2012; Miller et al., 2012).”
From Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears (2014) · cites this paper as Miller et al., 2012
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- Authors
- Miller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., Kim, H. L., Burhans, R. C., Drautz, D. I., Wittekindt, N. E., Tomsho, L. P., Ibarra-Laclette, E., Herrera-Estrella, L., Peacock, E., Farley, S., Sage, G. K., Rode, K., Obbard, M., Montiel, R., Bachmann, L., Ingólfsson, Ó., Aars, J., Mailund, T., Wiig, Ø., Talbot, S. L., & Lindqvist, C.
- Affiliations
- Pennsylvania State University (US)
- University at Buffalo, State University of New York (US)
- Nanyang Technological University (SG)
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36821, Mexico;
- United States Geological Survey (US)
- Alaska Department of Fish and Game (US)
- United States Fish and Wildlife Service (US)
- Ministry of Natural Resources and Forestry (CA)
- University of Oslo (NO)
- Department of Earth Sciences, University of Iceland, 101 Reykjavik, Iceland;
- Norwegian Polar Institute (NO)
- Aarhus University (DK)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-07-23
- Volume
- 109
- Issue
- 36
- Pages
- E2382-90
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3437856
- OpenAlex
- W2067218923
- Cited by
- 353
- References
- 62
- Citations by year
- 2026: 7 · 2025: 14 · 2024: 22 · 2023: 14 · 2022: 9 · 2021: 29 · 2020: 53 · 2019: 17 · 2018: 31 · 2017: 23 · 2016: 21 · 2015: 35 · 2014: 43 · 2013: 33 · 2012: 2
- FWCI
- 21.78
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DR-NTU (Nanyang Technological University) (submittedVersion)
- Funders
- National Science Foundation (0733029)
- Howard Hughes Medical Institute
- Massachusetts Department of Fish and Game
- Pennsylvania Department of Health
- University of Pennsylvania
- Aarhus Universitet
- Ministry of Natural Resources
- Alaska Department of Fish and Game
- Pennsylvania State University
- Penn State Clinical and Translational Science Institute
- Uppsala Universitet
- National Institutes of Health (UL1TR000127)
- U.S. Fish and Wildlife Service
- U.S. Geological Survey
- University at Buffalo
- National Center for Research Resources (UL1RR033184)
- National Center for Advancing Translational Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- polar bear, brown bear, Ursus americanus, species divergence, species tree, paleodemography, effective population size decline, climate change, Arctic adaptation, mitochondrial genome, nuclear genome
- MeSH terms
- Adaptation, Biological, Animals, Arctic Regions, Base Sequence, Ursidae, Genetic Markers, Genetics, Population, Molecular Sequence Data, Population Density, Population Dynamics, Species Specificity, Genome, Sequence Analysis, DNA, Evolution, Molecular, History, Ancient, Climate Change
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